NIMH Data Archive - Data

Genomics

Neuroimaging

Phenotype¹

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Clinical Trial

¹ Numbers reported are subjects by age

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Grant/Project Number

Format should be in the following format: Activity Code, Institute Abbreviation, and Serial Number. Grant Type, Support Year, and Suffix should be excluded. For example, grant 1R01MH123456-01A1 should be entered R01MH123456

Collection - Use Existing Experiment

To associate an experiment to the current collection, just select an axperiment from the table below then click the associate experiment button to persist your changes (saving the collection is not required). Note that once an experiment has been associated to two or more collections, the experiment will not longer be editable.

The table search feature is case insensitive and targets the experiment id, experiment name and experiment type columns. The experiment id is searched only when the search term entered is a number, and filtered using a startsWith comparison. When the search term is not numeric the experiment name is used to filter the results.

Select	Experiment Id	Experiment Name	Experiment Type	Created On

24	HI-NGS_R1	Omics	02/16/2011
475	MB1-10 (CHOP)	Omics	06/07/2016
490	Discovery and CRISPR validation of genetic factors associated with antipsychotic-induced weight gain and cardiometabolic risk	Omics	07/07/2016
501	PharmacoBOLD Resting State	fMRI	07/27/2016
506	PVPREF	Omics	08/05/2016
509	ABC-CT Resting v2	EEG	08/18/2016
13	Comparison of FI expression in Autistic and Neurotypical Homo Sapiens	Omics	12/28/2010
18	AGRE/Broad Affymetrix 5.0 Genotype Experiment	Omics	01/06/2011
22	Stitching PCR Sequencing	Omics	02/14/2011
26	ASD_Methylation	Omics	03/01/2011
29	Microarray family 03 (father, mother, sibling)	Omics	03/24/2011
37	Standard paired-end sequencing of BCRs	Omics	04/19/2011
38	Illumina Mate-Pair BCR sequencing	Omics	04/19/2011
39	Custom Jumping Libraries	Omics	04/19/2011
40	Custom CapBP	Omics	04/19/2011
41	Immunofluorescence	Omics	05/11/2011
43	Autism brain sample genotyping, Illumina	Omics	05/16/2011
47	ARRA Autism Sequencing Collaboration at Baylor. SOLiD 4 System	Omics	08/01/2011
53	AGRE Omni1-quad	Omics	10/11/2011
59	AGP genotyping	Omics	04/03/2012
60	Ultradeep 454 sequencing of synaptic genes from postmortem cerebella of individuals with ASD and neurotypical controls	Omics	06/23/2012
63	Microemulsion PCR and Targeted Resequencing for Variant Detection in ASD	Omics	07/20/2012
76	Whole Genome Sequencing in Autism Families	Omics	01/03/2013
519	Resting	fMRI	11/08/2016
90	Genotyped IAN Samples	Omics	07/09/2013
91	NJLAGS Axiom Genotyping Array	Omics	07/16/2013
93	AGP genotyping (CNV)	Omics	09/06/2013
106	Longitudinal Sleep Study. H20 200. Channel set 2	EEG	11/07/2013
107	Longitudinal Sleep Study. H20 200. Channel set 3	EEG	11/07/2013
108	Longitudinal Sleep Study. AURA 200	EEG	11/07/2013
105	Longitudinal Sleep Study. H20 200. Channel set 1	EEG	11/07/2013
109	Longitudinal Sleep Study. AURA 400	EEG	11/07/2013
116	Gene Expression Analysis WG-6	Omics	01/07/2014
131	Jeste Lab UCLA ACEii: Charlie Brown and Sesame Street - Project 1	Eye Tracking	02/27/2014
132	Jeste Lab UCLA ACEii: Animacy - Project 1	Eye Tracking	02/27/2014
133	Jeste Lab UCLA ACEii: Mom Stranger - Project 2	Eye Tracking	02/27/2014
134	Jeste Lab UCLA ACEii: Face Emotion - Project 3	Eye Tracking	02/27/2014
145	AGRE/FMR1_Illumina.JHU	Omics	04/14/2014
146	AGRE/MECP2_Sanger.JHU	Omics	04/14/2014
147	AGRE/MECP2_Junior.JHU	Omics	04/14/2014
151	Candidate Gene Identification in familial Autism	Omics	06/09/2014
152	NJLAGS Whole Genome Sequencing	Omics	07/01/2014
154	Math Autism Study - Vinod Menon	fMRI	07/15/2014
155	Resting	fMRI	07/25/2014
156	Speech	fMRI	07/25/2014
159	Emotion	fMRI	07/25/2014
160	syllable contrast	EEG	07/29/2014
167	School-age naturalistic stimuli	Eye Tracking	09/19/2014
44	AGRE/Broad Affymetrix 5.0 Genotype Experiment	Omics	06/27/2011
45	Exome Sequencing of 20 Sporadic Cases of Autism Spectrum Disorder	Omics	07/15/2011

Collection - Add Experiment

Add Supporting Documentation

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URL:

To add an existing Data Structure, enter its title in the search bar. If you need to request changes, select the indicator "No, it requires changes to meet research needs" after selecting the Structure, and upload the file with the request changes specific to the selected Data Structure. Your file should follow the Request Changes Procedure. If the Data Structure does not exist, select "Request New Data Structure" and upload the appropriate zip file.

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3/3-Schizophrenia Genetics and Brain Somatic Mosaicism #2963

General
Experiments (3)
Shared Data
Publications (35)
Data Expected (3)
Associated Studies (2)

Collection Title	Collection Investigators	Collection Description
Collection Title:	3/3-Schizophrenia Genetics and Brain Somatic Mosaicism
Collection Investigators:	Fred H. Gage
Collection Description:	Schizophrenia (SCZD) is a debilitating and typically incurable neuropsychiatric disease that affects 1% of the human population. Disease symptoms, which include hallucinations, paranoia, and impaired cognition, are thought to arise from impairments in neuronal connectivity and plasticity, but etiology of these defects remains unclear. Multiple lines of evidence suggest a strong genetic component to SCZD. Thus, identifying genetic variants associated with SCZD may provide critical tools for understanding and treating the disease. Indeed, recent genome wide association studies have identified >100 loci that are associated with SCZD, but these genetic variants account for only a small percentage of disease incidence. One potential explanation for this unsatisfying result is that SCZD risk alleles are not inherited through the germline, but instead arise through somatic mutations within neurons of affected individuals. Perhaps it is the propensity for somatic mosaicism that is inherited in patients with SCZD. It is now clear that somatic mosaicism of DNA sequence is much more common than previously thought (i.e., all cells within an individual do not contain the same genome), and that this phenomenon is particularly prevalent in the brain. These genomic differences may contribute to the diversity of neuronal function. However, dysregulation of processes that generate or control somatic mosaicism may lead to disease-related genomic instability. Our hypothesis, therefore, is that somatic mosaicism in neurons or their progenitors are a major contributor to SCZD pathogenesis. Aim 1 will use single-cell genomic sequencing techniques to identify somatic copy number variants (CNVs) in neuronal and non-neuronal cell types from patients with SCZD or neurotypic controls. These analyses will focus on the frontal cortex and hippocampus, two brain regions associated with SCZD pathogenesis. Results will determine whether somatic CNVs are overrepresented in SCZD brains, and whether SCZD risk alleles are disproportionately affected by these CNVs. Aim 2 will characterize somatic retrotransposon insertions within these same cell types, asking whether the frequency or location of retrotransposition events is altered in neurons from patients with SCZD compared with controls. A total of 8000 neurons will be analyzed in Aims 1 and 2, making this the most comprehensive analysis of neuronal somatic mosaicism to date. In Aim 3, genomic variants most overrepresented in patients with SCZD (identified in Aims 1 and 2) will be engineered into hESCs for functional validation tests. It has been shown that cultured neurons derived from patients with SCZD exhibit reduced levels of connectivity and have underdeveloped neurites compared with controls. Similar analyses will be performed using isogenic and mosaic cultures of neurons derived from engineered hESCs. Results from these studies will determine whether the level, pattern, or type of somatic mosaicism is altered in SCZD neurons, and potentially identify genes and gene networks most affected by these changes. Identifying causal disease factors will provide new therapeutic targets and move us closer to finding a cure for this devastating disease.
Data Repository:	NIMH Data Archive
Permission Group:
Collection Creation Date:	07/10/2018
NIH Research Initiative:	Brain Somatic Mosaicism Network (BSMN)
Collection Phase:	Funding Completed
Collection Sub-Phase:	Close Out
Blinded Clinical Trial:	No
Total Funded Amount:	$1,964,502.00
Subjects Shared:	27
Collection DOI:	10.15154/p88h-w120

{"values":[]}

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Funding Sources:

Funding Source Name	Funding Source URL
NIH - Extramural	None

Supporting Documentation:

Grant Information:

Project Number	Title	Start Date	Original End Date	End Date	Planned Enrollment	Actual Enrollment	Organization	Funds Obligated
U01MH106882-01	3/3-Schizophrenia Genetics and Brain Somatic Mosaicism	04/20/2015	01/31/2020	01/31/2020	Not Reported	Not Reported	SALK INSTITUTE FOR BIOLOGICAL STUDIES	$1,964,502.00

Clinical Trials:

helpcenter.collection.general-tab

Collection - General Tab

Fields available for edit on the top portion of the page include:

Collection Title
Investigators
Collection Description
Collection Phase
Funding Source
Clinical Trials

Collection Phase: The current status of a research project submitting data to an NDA Collection, based on the timing of the award and/or the data that have been submitted.

Pre-Enrollment: The default entry made when the NDA Collection is created.
Enrolling: Data have been submitted to the NDA Collection or the NDA Data Expected initial submission date has been reached for at least one data structure category in the NDA Collection.
Data Analysis: Subject level data collection for the research project is completed and has been submitted to the NDA Collection. The NDA Collection owner or the NDA Help Desk may set this phase when they’ve confirmed data submission is complete and submitted subject counts match at least 90% of the target enrollment numbers in the NDA Data Expected. Data submission reminders will be turned off for the NDA Collection.
Funding Completed: The NIH grant award (or awards) associated with the NDA Collection has reached its end date. NDA Collections in Funding Completed phase are assigned a subphase to indicate the status of data submission.
- The Data Expected Subphase indicates that NDA expects more data will be submitted
- The Closeout Subphase indicates the data submission is complete.
- The Sharing Not Met Subphase indicates that data submission was not completed as expected.

Blinded Clinical Trial Status:

This status is set by a Collection Owner and indicates the research project is a double blinded clinical trial. When selected, the public view of Data Expected will show the Data Expected items and the Submission Dates, but the targeted enrollment and subjects submitted counts will not be displayed.
Targeted enrollment and subjects submitted counts are visible only to NDA Administrators and to the NDA Collection or as the NDA Collection Owner.
When an NDA Collection that is flagged Blinded Clinical Trial reaches the maximum data sharing date for that Data Repository (see https://nda.nih.gov/nda/sharing-regimen.html), the embargo on Data Expected information is released.

Funding Source

The organization(s) responsible for providing the funding is listed here.

Supporting Documentation

Users with Submission privileges, as well as Collection Owners, Program Officers, and those with Administrator privileges, may upload and attach supporting documentation. By default, supporting documentation is shared to the general public, however, the option is also available to limit this information to qualified researchers only.

Grant Information

Identifiable details are displayed about the Project of which the Collection was derived from. You may click in the Project Number to view a full report of the Project captured by the NIH.

Clinical Trials

Any data that is collected to support or further the research of clinical studies will be available here. Collection Owners and those with Administrator privileges may add new clinical trials.

Frequently Asked Questions

How does the NIMH Data Archive (NDA) determine which Permission Group data are submitted into?

During Collection creation, NDA staff determine the appropriate Permission Group based on the type of data to be submitted, the type of access that will be available to data access users, and the information provided by the Program Officer during grant award.
How do I know when a NDA Collection has been created?

When a Collection is created by NDA staff, an email notification will automatically be sent to the PI(s) of the grant(s) associated with the Collection to notify them.
Is a single grant number ever associated with more than one Collection?

The NDA system does not allow for a single grant to be associated with more than one Collection; therefore, a single grant will not be listed in the Grant Information section of a Collection for more than one Collection.
Why is there sometimes more than one grant included in a Collection?

In general, each Collection is associated with only one grant; however, multiple grants may be associated if the grant has multiple competing segments for the same grant number or if multiple different grants are all working on the same project and it makes sense to hold the data in one Collection (e.g., Cooperative Agreements).

Glossary

Administrator Privilege

A privilege provided to a user associated with an NDA Collection or NDA Study whereby that user can perform a full range of actions including providing privileges to other users.
Collection Owner

Generally, the Collection Owner is the contact PI listed on a grant. Only one NDA user is listed as the Collection owner. Most automated emails are primarily sent to the Collection Owner.
Collection Phase
The Collection Phase provides information on data submission as opposed to grant/project completion so while the Collection phase and grant/project phase may be closely related they are often different. Collection users with Administrative Privileges are encouraged to edit the Collection Phase. The Program Officer as listed in eRA (for NIH funded grants) may also edit this field. Changes must be saved by clicking the Save button at the bottom of the page. This field is sortable alphabetically in ascending or descending order. Collection Phase options include:
- Pre-Enrollment: A grant/project has started, but has not yet enrolled subjects.
- Enrolling: A grant/project has begun enrolling subjects. Data submission is likely ongoing at this point.
- Data Analysis: A grant/project has completed enrolling subjects and has completed all data submissions.
- Funding Completed: A grant/project has reached the project end date.
Collection Title

An editable field with the title of the Collection, which is often the title of the grant associated with the Collection.
Grant

Provides the grant number(s) for the grant(s) associated with the Collection. The field is a hyperlink so clicking on the Grant number will direct the user to the grant information in the NIH Research Portfolio Online Reporting Tools (RePORT) page.
Supporting Documentation

Various documents and materials to enable efficient use of the data by investigators unfamiliar with the project and may include the research protocol, questionnaires, and study manuals.
NIH Research Initiative

NDA Collections may be organized by scientific similarity into NIH Research Initiatives, to facilitate query tool user experience. NIH Research Initiatives map to one or multiple Funding Opportunity Announcements.
Permission Group

Access to shared record-level data in NDA is provisioned at the level of a Permission Group. NDA Permission Groups consist of one or multiple NDA Collections that contain data with the same subject consents.
Planned Enrollment

Number of human subject participants to be enrolled in an NIH-funded clinical research study. The data is provided in competing applications and annual progress reports.
Actual Enrollment

Number of human subjects enrolled in an NIH-funded clinical research study. The data is provided in annual progress reports.
NDA Collection

A virtual container and organization structure for data and associated documentation from one grant or one large project/consortium. It contains tools for tracking data submission and allows investigators to define a wide array of other elements that provide context for the data, including all general information regarding the data and source project, experimental parameters used to collect any event-based data contained in the Collection, methods, and other supporting documentation. They also allow investigators to link underlying data to an NDA Study, defining populations and subpopulations specific to research aims.
Data Use Limitations

Data Use Limitations (DULs) describe the appropriate secondary use of a dataset and are based on the original informed consent of a research participant. NDA only accepts consent-based data use limitations defined by the NIH Office of Science Policy.
Total Subjects Shared

The total number of unique subjects for whom data have been shared and are available for users with permission to access data.

Contact NDA Help Desk

ID	Name	Created Date	Status	Type
915	Virginia_single_cell_MiSeq	05/03/2018	Approved	Omics
916	Virginia_single_cell_HiSeq2500	05/03/2018	Approved	Omics
917	Virginia_single_cell_HiSeq3000	05/03/2018	Approved	Omics

helpcenter.collection.experiments-tab

Collection - Experiments

The number of Experiments included is displayed in parentheses next to the tab name. You may download all experiments associated with the Collection via the Download button. You may view individual experiments by clicking the Experiment Name and add them to the Filter Cart via the Add to Cart button.

Collection Owners, Program Officers, and users with Submission or Administrative Privileges for the Collection may create or edit an Experiment.

Please note: The creation of an NDA Experiment does not necessarily mean that data collected, according to the defined Experiment, has been submitted or shared.

Frequently Asked Questions

Can an Experiment be associated with more than one Collection?
Yes -see the “Copy” button in the bottom left when viewing an experiment. There are two actions that can be performed via this button:
1. Copy the experiment with intent for modifications.
2. Associate the experiment to the collection. No modifications can be made to the experiment.

Glossary

Experiment Status

An Experiment must be Approved before data using the associated Experiment_ID may be uploaded.
Experiment ID

The ID number automatically generated by NDA which must be included in the appropriate file when uploading data to link the Experiment Definition to the subject record.

Contact NDA Help Desk

Shared Data:

Title	Type	Number of Subjects
Brain and Tissue Bank Form	Clinical Assessments	6
Genomics Sample	Genomics	27
Genomics Subject	Genomics	6

helpcenter.collection.shared-data-tab

Collection - Shared Data

This tab provides a quick overview of the Data Structure title, Data Type, and Number of Subjects that are currently Shared for the Collection. The information presented in this tab is automatically generated by NDA and cannot be edited. If no information is visible on this tab, this would indicate the Collection does not have shared data or the data is private.

The shared data is available to other researchers who have permission to access data in the Collection's designated Permission Group(s). Use the Download button to get all shared data from the Collection to the Filter Cart.

Frequently Asked Questions

How will I know if another researcher uses data that I shared through the NIMH Data Archive (NDA)?

To see what data your project have submitted are being used by a study, simply go the Associated Studies tab of your collection. Alternatively, you may review an NDA Study Attribution Report available on the General tab.
Can I get a supplement to share data from a completed research project?

Often it becomes more difficult to organize and format data electronically after the project has been completed and the information needed to create a GUID may not be available; however, you may still contact a program staff member at the appropriate funding institution for more information.
Can I get a supplement to share data from a research project that is still ongoing?

Unlike completed projects where researchers may not have the information needed to create a GUID and/or where the effort needed to organize and format data becomes prohibitive, ongoing projects have more of an opportunity to overcome these challenges. Please contact a program staff member at the appropriate funding institution for more information.

Glossary

Data Structure

A defined organization and group of Data Elements to represent an electronic definition of a measure, assessment, questionnaire, or collection of data points. Data structures that have been defined in the NDA Data Dictionary are available at https://nda.nih.gov/general-query.html?q=query=data-structure
Data Type

A grouping of data by similar characteristics such as Clinical Assessments, Omics, or Neurosignal data.
Shared

The term 'Shared' generally means available to others; however, there are some slightly different meanings based on what is Shared. A Shared NDA Study is viewable and searchable publicly regardless of the user's role or whether the user has an NDA account. A Shared NDA Study does not necessarily mean that data used in the NDA Study have been shared as this is independently determined. Data are shared according the schedule defined in a Collection's Data Expected Tab and/or in accordance with data sharing expectations in the NDA Data Sharing Terms and Conditions. Additionally, Supporting Documentation uploaded to a Collection may be shared independent of whether data are shared.

Contact NDA Help Desk

Collection Owners and those with Collection Administrator permission, may edit a collection. The following is currently available for Edit on this page:

Publications

Publications relevant to NDA data are listed below. Most displayed publications have been associated with the grant within Pubmed. Use the "+ New Publication" button to add new publications. Publications relevant/not relevant to data expected are categorized. Relevant publications are then linked to the underlying data by selecting the Create Study link. Study provides the ability to define cohorts, assign subjects, define outcome measures and lists the study type, data analysis and results. Analyzed data and results are expected in this way.

PubMed ID	Study	Title	Journal	Authors	Date	Status
38760338	Create Study	Mapping recurrent mosaic copy number variation in human neurons.	Nature communications	Sun, Chen; Kathuria, Kunal; Emery, Sarah B; Kim, ByungJun; Burbulis, Ian E; Shin, Joo Heon; Brain Somatic Mosaicism Network; Weinberger, Daniel R; Moran, John V; Kidd, Jeffrey M; Mills, Ryan E; McConnell, Michael J	May 17, 2024	Not Determined
38349791	Create Study	Long interspersed nuclear elements safeguard neural progenitors from precocious differentiation.	Cell reports	Toda, Tomohisa; Bedrosian, Tracy A; Schafer, Simon T; Cuoco, Michael S; Linker, Sara B; Ghassemzadeh, Saeed; Mitchell, Lisa; Whiteley, Jack T; Novaresi, Nicole; McDonald, Aidan H; Gallina, Iryna S; Yoon, Hyojung; Hester, Mark E; Pena, Monique; Lim, Christina; Suljic, Emelia; AlFatah Mansour, Abed; Boulard, Matthieu; Parylak, Sarah L; Gage, Fred H	February 27, 2024	Not Determined
37985666	Create Study	Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases.	Scientific data	Garrison, McKinzie A; Jang, Yeongjun; Bae, Taejeong; Cherskov, Adriana; Emery, Sarah B; Fasching, Liana; Jones, Attila; Moldovan, John B; Molitor, Cindy; Pochareddy, Sirisha; Peters, Mette A; Shin, Joo Heon; Wang, Yifan; Yang, Xiaoxu; Akbarian, Schahram; Chess, Andrew; Gage, Fred H; Gleeson, Joseph G; Kidd, Jeffrey M; McConnell, Michael; Mills, Ryan E; Moran, John V; Park, Peter J; Sestan, Nenad; Urban, Alexander E; Vaccarino, Flora M; Walsh, Christopher A; Weinberger, Daniel R; Wheelan, Sarah J; Abyzov, Alexej; BSMN Consortium	November 20, 2023	Not Determined
35901164	Create Study	Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability.	Science (New York, N.Y.)	Bae, Taejeong; Fasching, Liana; Wang, Yifan; Shin, Joo Heon; Suvakov, Milovan; Jang, Yeongjun; Norton, Scott; Dias, Caroline; Mariani, Jessica; Jourdon, Alexandre; Wu, Feinan; Panda, Arijit; Pattni, Reenal; Chahine, Yasmine; Yeh, Rebecca; Roberts, Rosalinda C; Huttner, Anita; Kleinman, Joel E; Hyde, Thomas M; Straub, Richard E; Walsh, Christopher A; Brain Somatic Mosaicism Network§; Urban, Alexander E; Leckman, James F; Weinberger, Daniel R; Vaccarino, Flora M; Abyzov, Alexej	July 29, 2022	Not Determined
33781308	Create Study	Comprehensive identification of somatic nucleotide variants in human brain tissue.	Genome biology	Wang, Yifan; Bae, Taejeong; Thorpe, Jeremy; Sherman, Maxwell A; Jones, Attila G; Cho, Sean; Daily, Kenneth; Dou, Yanmei; Ganz, Javier; Galor, Alon; Lobon, Irene; Pattni, Reenal; Rosenbluh, Chaggai; Tomasi, Simone; Tomasini, Livia; Yang, Xiaoxu; Zhou, Bo; Akbarian, Schahram; Ball, Laurel L; Bizzotto, Sara; Emery, Sarah B; Doan, Ryan; Fasching, Liana; Jang, Yeongjun; Juan, David; Lizano, Esther; Luquette, Lovelace J; Moldovan, John B; Narurkar, Rujuta; Oetjens, Matthew T; Rodin, Rachel E; Sekar, Shobana; Shin, Joo Heon; Soriano, Eduardo; Straub, Richard E; Zhou, Weichen; Chess, Andrew; Gleeson, Joseph G; Marquès-Bonet, Tomas; Park, Peter J; Peters, Mette A; Pevsner, Jonathan; Walsh, Christopher A; Weinberger, Daniel R; Brain Somatic Mosaicism Network; Vaccarino, Flora M; Moran, John V; Urban, Alexander E; Kidd, Jeffrey M; Mills, Ryan E; Abyzov, Alexej	March 29, 2021	Not Determined
33432196	Create Study	Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia.	Nature neuroscience	Zhu, Xiaowei; Zhou, Bo; Pattni, Reenal; Gleason, Kelly; Tan, Chunfeng; Kalinowski, Agnieszka; Sloan, Steven; Fiston-Lavier, Anna-Sophie; Mariani, Jessica; Petrov, Dmitri; Barres, Ben A; Duncan, Laramie; Abyzov, Alexej; Vogel, Hannes; Brain Somatic Mosaicism Network; Moran, John V; Vaccarino, Flora M; Tamminga, Carol A; Levinson, Douglas F; Urban, Alexander E	February 1, 2021	Not Determined
33432195	Create Study	The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing.	Nature neuroscience	Rodin, Rachel E; Dou, Yanmei; Kwon, Minseok; Sherman, Maxwell A; D'Gama, Alissa M; Doan, Ryan N; Rento, Lariza M; Girskis, Kelly M; Bohrson, Craig L; Kim, Sonia N; Nadig, Ajay; Luquette, Lovelace J; Gulhan, Doga C; Brain Somatic Mosaicism Network; Park, Peter J; Walsh, Christopher A	February 1, 2021	Not Determined
33398186	Create Study	Quantum computing at the frontiers of biological sciences.	Nature methods	Emani, Prashant S; Warrell, Jonathan; Anticevic, Alan; Bekiranov, Stefan; Gandal, Michael; McConnell, Michael J; Sapiro, Guillermo; Aspuru-Guzik, Alán; Baker, Justin T; Bastiani, Matteo; Murray, John D; Sotiropoulos, Stamatios N; Taylor, Jacob; Senthil, Geetha; Lehner, Thomas; Gerstein, Mark B; Harrow, Aram W	July 1, 2021	Not Determined
33122305	Create Study	Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus.	Genome research	Linker, Sara B; Randolph-Moore, Lynne; Kottilil, Kalyani; Qiu, Fan; Jaeger, Baptiste N; Barron, Jerika; Gage, Fred H	November 1, 2020	Not Determined
32879908	Create Study	Implementation of a Hamming distance-like genomic quantum classifier using inner products on ibmqx2 and ibmq_16_melbourne.	Quantum machine intelligence	Kathuria, Kunal; Ratan, Aakrosh; McConnell, Michael; Bekiranov, Stefan	January 1, 2020	Not Determined
32446240	Create Study	Generation of four postmortem dura-derived iPS cell lines from four control individuals with genotypic and brain-region-specific transcriptomic data available through the BrainSEQ consortium.	Stem cell research	Sawada, Tomoyo; Benjamin, Kynon J M; Brandtjen, Anna C; Tietze, Ethan; Allen, Samuel J; Paquola, Apuã C M; Kleinman, Joel E; Hyde, Thomas M; Erwin, Jennifer A	July 1, 2020	Not Determined
32179177	Create Study	A deletion in Eml1 leads to bilateral subcortical heterotopia in the tish rat.	Neurobiology of disease	Grosenbaugh, Denise K; Joshi, Suchitra; Fitzgerald, Mark P; Lee, Kevin S; Wagley, Pravin K; Koeppel, Alexander F; Turner, Stephen D; McConnell, Michael J; Goodkin, Howard P	July 2020	Not Determined
32041882	Create Study	Synaptotagmin-7 is a key factor for bipolar-like behavioral abnormalities in mice.	Proceedings of the National Academy of Sciences of the United States of America	Shen W, Wang QW, Liu YN, Marchetto MC, Linker S, Lu SY, Chen Y, Liu C, Guo C, Xing Z, Shi W, Kelsoe JR, Alda M, Wang H, Zhong Y, Sui SF, Zhao M, Yang Y, Mi S, Cao L, Gage FH, Yao J	February 2020	Not Determined
32004479	Create Study	Increased Neural Progenitor Proliferation in a hiPSC Model of Autism Induces Replication Stress-Associated Genome Instability.	Cell stem cell	Wang, Meiyan; Wei, Pei-Chi; Lim, Christina K; Gallina, Iryna S; Marshall, Sara; Marchetto, Maria C; Alt, Frederick W; Gage, Fred H	February 2020	Not Determined
31767646	Create Study	Modeling Brain Disorders Using Induced Pluripotent Stem Cells.	Cold Spring Harbor perspectives in biology	Vadodaria, Krishna C; Jones, Jeffrey R; Linker, Sara; Gage, Fred H	June 1, 2020	Not Determined
31134525	Create Study	Modeling neuropsychiatric disorders using human induced pluripotent stem cells.	Protein & cell	Wang, Meiyan; Zhang, Lei; Gage, Fred H	January 2020	Not Determined
30673605	Create Study	Neurons with Complex Karyotypes Are Rare in Aged Human Neocortex.	Cell reports	Chronister, William D; Burbulis, Ian E; Wierman, Margaret B; Wolpert, Matthew J; Haakenson, Mark F; Smith, Aiden C B; Kleinman, Joel E; Hyde, Thomas M; Weinberger, Daniel R; Bekiranov, Stefan; McConnell, Michael J	January 2019	Not Determined
30406823	Create Study	The effect of rho kinase inhibition on morphological and electrophysiological maturity in iPSC-derived neurons.	Cell and tissue research	Harbom, Lise J; Rudisill, Taylor L; Michel, Nadine; Litwa, Karen A; Beenhakker, Mark P; McConnell, Michael J	March 2019	Not Determined
30381404	Create Study	Adult Hippocampal Neurogenesis: A Coming-of-Age Story.	The Journal of neuroscience : the official journal of the Society for Neuroscience	Kuhn HG, Toda T, Gage FH	December 2018	Not Relevant
30147644	Create Study	Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells.	Frontiers in molecular neuroscience	van den Hurk, Mark; Erwin, Jennifer A; Yeo, Gene W; Gage, Fred H; Bardy, Cedric	January 2018	Not Determined
30055482	Create Study	Improved molecular karyotyping in glioblastoma.	Mutation research	Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, Mcconnell MJ	September 2018	Not Determined
29727680	Create Study	Efficient Generation of CA3 Neurons from Human Pluripotent Stem Cells Enables Modeling of Hippocampal Connectivity In Vitro.	Cell stem cell	Sarkar, Anindita; Mei, Arianna; Paquola, Apua C M; Stern, Shani; Bardy, Cedric; Klug, Jason R; Kim, Stacy; Neshat, Neda; Kim, Hyung Joon; Ku, Manching; Shokhirev, Maxim N; Adamowicz, David H; Marchetto, Maria C; Jappelli, Roberto; Erwin, Jennifer A; Padmanabhan, Krishnan; Shtrahman, Matthew; Jin, Xin; Gage, Fred H	May 2018	Not Determined
29679070	Create Study	The role of adult hippocampal neurogenesis in brain health and disease.	Molecular psychiatry	Toda T, Parylak SL, Linker SB, Gage FH	April 2018	Not Determined
29658944	Create Study	An in vivo model of functional and vascularized human brain organoids.	Nature biotechnology	Mansour, Abed AlFatah; Gonçalves, J Tiago; Bloyd, Cooper W; Li, Hao; Fernandes, Sarah; Quang, Daphne; Johnston, Stephen; Parylak, Sarah L; Jin, Xin; Gage, Fred H	June 2018	Not Determined
29567711	Create Study	Early life experience drives structural variation of neural genomes in mice.	Science (New York, N.Y.)	Bedrosian TA, Quayle C, Novaresi N, Gage FH	March 2018	Not Determined

helpcenter.collection.publications-tab

Collection - Publications

The number of Publications is displayed in parentheses next to the tab name. Clicking on any of the Publication Titles will open the Publication in a new internet browsing tab.

Collection Owners, Program Officers, and users with Submission or Administrative Privileges for the Collection may mark a publication as either Relevant or Not Relevant in the Status column.

Frequently Asked Questions

How can I determine if a publication is relevant?

Publications are considered relevant to a collection when the data shared is directly related to the project or collection.
Where does the NDA get the publications?

PubMed, an online library containing journals, articles, and medical research. Sponsored by NiH and National Library of Medicine (NLM).

Glossary

Create Study

A link to the Create an NDA Study page that can be clicked to start creating an NDA Study with information such as the title, journal and authors automatically populated.
Not Determined Publication

Indicates that the publication has not yet been reviewed and/or marked as Relevant or Not Relevant so it has not been determined whether an NDA Study is expected.
Not Relevant Publication

A publication that is not based on data related to the aims of the grant/project associated with the Collection or not based on any data such as a review article and, therefore, an NDA Study is not expected to be created.
PubMed

PubMed provides citation information for biomedical and life sciences publications and is managed by the U.S. National Institutes of Health's National Library of Medicine.
PubMed ID

The PUBMed ID is the unique ID number for the publication as recorded in the PubMed database.
Relevant Publication

A publication that is based on data related to the aims of the grant/project associated with the Collection and, therefore, an NDA Study is expected to be created.

Contact NDA Help Desk

Data Expected List: Mandatory Data Structures

These data structures are mandatory for your NDA Collection. Please update the Targeted Enrollment number to accurately represent the number of subjects you expect to submit for the entire study.

For NIMH HIV-related research that involves human research participants: Select the dictionary or dictionaries most appropriate for your research. If your research does not require all three data dictionaries, just ignore the ones you do not need. There is no need to delete extra data dictionaries from your NDA Collection. You can adjust the Targeted Enrollment column in the Data Expected tab to “0” for those unnecessary data dictionaries. At least one of the three data dictionaries must have a non-zero value.

Data Expected	Targeted Enrollment	Initial Submission	Subjects Submitted	Initial Share	Subjects Shared	Status
Genomics/omics	6	01/15/2019	27	05/15/2019	27	Approved
Research Subject and Pedigree	38	01/15/2019	6	05/15/2019	6	Approved

To create your project's Data Expected list, use the "+New Data Expected" to add or request existing structures and to request new Data Structures that are not in the NDA Data Dictionary.

If the Structure you need already exists, locate it and specify your dates and enrollment when adding it to your Data Expected list. If you require changes to the Structure you need, select the indicator stating "No, it requires changes to meet research needs," and upload a file containing your requested changes.

If the structure you need is not yet defined in the Data Dictionary, you can select "Upload Definition" and attach the necessary materials to request its creation.

When selecting the expected dates for your data, make sure to follow the standard Data Sharing Regimen and choose dates within the date ranges that correspond to your project start and end dates.

Please visit the Completing Your Data Expected Tutorial for more information.

Data Expected List: Data Structures per Research Aims

These data structures are specific to your research aims and should list all data structures in which data will be collected and submitted for this NDA Collection. Please update the Targeted Enrollment number to accurately represent the number of subjects you expect to submit for the entire study.

Data Expected	Targeted Enrollment	Initial Submission	Subjects Submitted	Initial Share	Subjects Shared	Status
Summary	6	01/15/2019	6	05/15/2019	6	Approved

Structure not yet defined

No Status history for this Data Expected has been recorded yet

helpcenter.collection.data-expected-tab

Collection - Data Expected

The Data Expected tab displays the list of all data that NDA expects to receive in association with the Collection as defined by the contributing researcher, as well as the dates for the expected initial upload of the data, and when it is first expected to be shared, or with the research community. Above the primary table of Data Expected, any publications determined to be relevant to the data within the Collection are also displayed - members of the contributing research group can use these to define NDA Studies, connecting those papers to underlying data in NDA.

The tab is used both as a reference for those accessing shared data, providing information on what is expected and when it will be shared, and as the primary tracking mechanism for contributing projects. It is used by both contributing primary researchers, secondary researchers, and NIH Program and Grants Management staff.

Researchers who are starting their project need to update their Data Expected list to include all the Data Structures they are collecting under their grant and set their initial submission and sharing schedule according to the NDA Data Sharing Regimen.

To add existing Data Structures from the Data Dictionary, to request new Data Structure that are not in the Dictionary, or to request changes to existing Data Structures, click "+New Data Expected".

For step-by-step instructions on how to add existing Data Structures, request changes to an existing Structure, or request a new Data Structure, please visit the Completing Your Data Expected Tutorial.

If you are a contributing researcher creating this list for the first time, or making changes to the list as your project progress, please note the following:

Although items you add to the list and changes you make are displayed, they are not committed to the system until you Save the entire page using the "Save" button at the bottom of your screen. Please Save after every change to ensure none of your work is lost.
If you attempt to add a new structure, the title you provide must be unique - if another structure exists with the same name your change will fail.
Adding a new structure to this list is the only way to request the creation of a new Data Dictionary definition.

Frequently Asked Questions

What is an NDA Data Structure?

An NDA Data Structure is comprised of multiple Data Elements to make up an electronic definition of an assessment, measure, questionnaire, etc will have a corresponding Data Structure.
What is the NDA Data Dictionary?

The NDA Data Dictionary is comprised of electronic definitions known as Data Structures.

Glossary

Analyzed Data

Data specific to the primary aims of the research being conducted (e.g. outcome measures, other dependent variables, observations, laboratory results, analyzed images, volumetric data, etc.) including processed images.
Data Item

Items listed on the Data Expected list in the Collection which may be an individual and discrete Data Structure, Data Structure Category, or Data Structure Group.
Data Structure

A defined organization and group of Data Elements to represent an electronic definition of a measure, assessment, questionnaire, or collection of data points. Data structures that have been defined in the NDA Data Dictionary are available at https://nda.nih.gov/general-query.html?q=query=data-structure
Data Structure Category

An NDA term describing the affiliation of a Data Structure to a Category, which may be disease/disorder or diagnosis related (Depression, ADHD, Psychosis), specific to data type (MRI, eye tracking, omics), or type of data (physical exam, IQ).
Data Structure Group

A Data Item listed on the Data Expected tab of a Collection that indicates a group of Data Structures (e.g., ADOS or SCID) for which data may be submitted instead of a specific Data Structure identified by version, module, edition, etc. For example, the ADOS Data Structure Category includes every ADOS Data Structure such as ADOS Module 1, ADOS Module 2, ADOS Module 1 - 2nd Edition, etc. The SCID Data Structure Group includes every SCID Data Structure such as SCID Mania, SCID V Mania, SCID PTSD, SCID-V Diagnosis, and more.
Evaluated Data

A new Data Structure category, Evaluated Data is analyzed data resulting from the use of computational pipelines in the Cloud and can be uploaded directly back to a miNDAR database. Evaluated Data is expected to be listed as a Data Item in the Collection's Data Expected Tab.
Imaging Data

Imaging+ is an NDA term which encompasses all imaging related data including, but not limited to, images (DTI, MRI, PET, Structural, Spectroscopy, etc.) as well as neurosignal data (EEG, fMRI, MEG, EGG, eye tracking, etc.) and Evaluated Data.
Initial Share Date

Initial Submission and Initial Share dates should be populated according to the NDA Data Sharing Terms and Conditions. Any modifications to these will go through the approval processes outlined above. Data will be shared with authorized users upon publication (via an NDA Study) or 1-2 years after the grant end date specified on the first Notice of Award, as defined in the applicable Data Sharing Terms and Conditions.
Initial Submission Date

Initial Submission and Initial Share dates should be populated according to these NDA Data Sharing Terms and Conditions. Any modifications to these will go through the approval processes outlined above. Data for all subjects is not expected on the Initial Submission Date and modifications may be made as necessary based on the project's conduct.
Research Subject and Pedigree

An NDA created Data Structure used to convey basic information about the subject such as demographics, pedigree (links family GUIDs), diagnosis/phenotype, and sample location that are critical to allow for easier querying of shared data.
Submission Cycle

The NDA has two Submission Cycles per year - January 15 and July 15.
Submission Exemption

An interface to notify NDA that data may not be submitted during the upcoming/current submission cycle.

Contact NDA Help Desk

Collection Owners and those with Collection Administrator permission, may edit a collection. The following is currently available for Edit on this page:

Associated Studies

Studies that have been defined using data from a Collection are important criteria to determine the value of data shared. The number of subjects column displays the counts from this Collection that are included in a Study, out of the total number of subjects in that study. The Data Use column represents whether or not the study is a primary analysis of the data or a secondary analysis. State indicates whether the study is private or shared with the research community.

Study NameFilter by Study Name	DOIFilter by DOI	AbstractFilter by Abstract	Collection/Study SubjectsFilter by Collection/Study Subjects	Data UsageFilter by Data Usage	StateFilter by State
BSMN Comprehensive Data Collection	10.15154/1519293	Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that plays a crucial role in normal development and disease. To study the nature and extent of somatic mosaicism in autism spectrum disorder, bipolar disorder, focal cortical dysplasia, schizophrenia, and Tourette syndrome, a multi-institutional consortium called the Brain Somatic Mosaicism Network (BSMN) was formed through the National Institute of Mental Health (NIMH). In addition to genomic data of affected and neurotypical brains, the BSMN also developed and validated a best practices somatic single nucleotide variant calling workflow through the analysis of reference brain tissue. These resources, including >400 terabytes of data from over 1150 individuals, are now available to the research community NIMH Data Archive (NDA) and are described here.	27/1087	Secondary Analysis	Shared
Neurons with complex karyotypes are rare in aged human neocortex	10.15154/1503237	Megabase-scale somatic copy number variants (CNVs) lead to complex karyotypes that alter allelic diversity in a subset of human neocortical neurons. Reported frequencies of neurons with complex karyotypes range from ~5% of neurons in some individuals to greater than 30% in other individuals. Genome-wide and familial studies implicitly assume a constant brain genome when assessing the genetic risk architecture of neurological disease, thus it is critical to determine whether divergent levels of neurons with complex karyotypes (CNV neurons) reflect normal individual variation or technical differences between approaches. We developed a computational approach that measures single cell library quality based on Bayesian Information Criterion and identifies integer-like variant segments from population-level statistics. A brain CNV atlas was assembled using a new dataset (>800 neurons from 5 neurotypical individuals) and published data from 10 additional neurotypical individuals. This atlas reveals that the frequency of neocortical neurons with complex karyotypes varies widely among individuals, but that this variability is not readily accounted for by tissue quality or CNV detection approach. Rather, the age of the individual is anti-correlated with CNV neuron frequency. Fewer CNV neurons are observed in aged individuals than young individuals.	6/6	Primary Analysis	Shared

* Data not on individual level

helpcenter.collection.associated-studies-tab

Collection - Associated Studies

Clicking on the Study Title will open the study details in a new internet browser tab. The Abstract is available for viewing, providing the background explanation of the study, as provided by the Collection Owner.

Primary v. Secondary Analysis: The Data Usage column will have one of these two choices. An associated study that is listed as being used for Primary Analysis indicates at least some and potentially all of the data used was originally collected by the creator of the NDA Study. Secondary Analysis indicates the Study owner was not involved in the collection of data, and may be used as supporting data.

Private v. Shared State: Studies that remain private indicate the associated study is only available to users who are able to access the collection. A shared study is accessible to the general public.

Frequently Asked Questions

How do I associate a study to my collection?

Studies are associated to the Collection automatically when the data is defined in the Study.

Glossary

Associated Studies Tab

A tab in a Collection that lists the NDA Studies that have been created using data from that Collection including both Primary and Secondary Analysis NDA Studies.

Contact NDA Help Desk

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Associated Studies

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